Epigenomics

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The bioinformatics applications assigned the Biological domain Epigenomics ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 29 results.

	Biological domain	Bioinformatics method	Input format	Output format
BiQ Analyzer	DNA methylation Epigenomics
Bismark	Genomics DNA methylation Epigenomics	Read mapping Bisulfite mapping Methylation calling	FASTA FASTQ	SAM (or custom)
BRAT	DNA methylation Epigenomics	Bisulfite mapping Mapping
BS Seeker	Epigenomics	Bisulfite mapping
BS-Seq	Epigenomics	Bisulfite mapping
CHiCAGO	Epigenomics	Peak calling	BAM	SeqMonk IBed WashU
ChromHMM	Epigenomics	Statistical calculation
Epigenome	Epigenomics	Bisulfite mapping
EpiGRAPH	Epigenomics Machine learning	Statistical calculation
Geneious	Sequence assembly (de novo assembly) Genomics RNA-Seq Metagenomics Epigenomics Structural variation Sequence analysis Phylogenetics Population genetics	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery	FASTA FASTQ SAM ELAND GenBank CSFASTA CSQUAL
GimmeMotifs	ChIP-seq Epigenomics Gene regulation	Sequence motif comparison	FASTA BED	HTML PSSM
Golden Helix	Genomics SNP detection Epigenomics Sequencing Copy number estimation Data handling	Annotation Genome visualisation Sequencing quality control Sequence contamination filtering Variant calling Statistical calculation Collapsing methods Variant classification
GPS	Genomics ChIP-seq Epigenomics Transcription factors and regulatory sites	Peak calling	ELAND BED Bowtie SAM/BAM
Hicup	Epigenomics	Read mapping	FASTQ (Compressed) FASTQ	SAM/BAM
HINT	Epigenomics Transcription factors and regulatory sites Regulatory genomics	Peak calling Nucleic acid sequence feature detection	BAM BED	BED
IOmics	Genomics Transcriptomics ChIP-seq RNA-Seq Regulatory RNA Exome capture Epigenomics	Sequence assembly Sequence alignment Ab-initio gene prediction Variant calling MiRNA analysis Exome analysis
Kismeth	DNA methylation Epigenomics	Bisulfite mapping
MethMarker	DNA methylation Epigenomics
MethylCoder	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping	FASTA FASTQ	SAM TXT Binary
Ngs-pipeline	SNP detection Indel detection Epigenomics Structural variation Personalised medicine	Read mapping Sequence annotation	FASTQ BAM CSFASTA/CSQUAL (ABI SOLiD) (Compressed) FASTQ	BAM VCF
Ngs.plot	Transcriptomics Epigenomics	Visualisation	BAM	PDF ZIP
NPS	ChIP-seq Epigenomics
NucleR	ChIP-seq Epigenomics ChIP-on-chip DNA packaging	Peak calling Annotation	ShortRead BioConductor	BED WIG BioConductor
Partek Genomics Suite	Transcriptomics ChIP-seq SNP detection RNA-Seq quantification DNA transcription Epigenomics Alternative splicing Functional genomics
PASH	DNA methylation Epigenomics	Sequence alignment Bisulfite mapping
RSAT peak-motifs	ChIP-seq Epigenomics Gene regulation	Sequence motif recognition Sequence motif comparison Sequence motif discovery	Fasta	HTML Text Graphics (png)
SeqMonk	Genomics Epigenomics	Visualisation Sequence assembly visualisation Sequence alignment visualisation Statistical calculation	SAM BAM GFF BED Eland Maq Delimited Text Bowtie Bismark	Delimited Text PNG SVG
SICER	ChIP-seq Epigenomics	Sequence contamination filtering	BED	WIG
Syapse	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	VCF